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Author Topic: R-L21: New SNP Z253 found in Iberians, ancestral for L226  (Read 48038 times)
ironroad41
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« Reply #200 on: April 24, 2012, 07:24:48 AM »

....  I have done a TMRCA between the Clan Gregor Moderator and  myself and the Clan Gregor chieftain.  I used two approaches: for the moderator I compared 59 STR''s and used Chandlers and the set of 110 rates from 2011. I got c. 200 AD for Chandlers rates and c. 550BC for the 110 data set.  For the chieftain, I followed Busbys recommendation and only looked at the 13 slowest FtDNA markers which we differ at two: 388 and 495.   I got a TMRCA of c. 13k BC!! I personally believe that the Chief is of Hallstatt origin who migrated to what is now Belgium and then were ousted by the Romans and they migrated to Ireland, where they became what is now called South Irish and later Dal Riadans.....
Are the Gregor Moderator and Chieftain Z253?  If they aren't, your relationship to them has to be at least two thousand years ago.

As far as using only the 13 slowest markers, per Busby, I don't recommend that at all. That's just not enough markers and particularly since you are looking for relationships in the historical timeframe I don't think the linear duration of STRs will be a big problem in your analysis.

@IronR, Mike shows the age of Z253 is around 400BC to 0AD leaving about 1500 years to L21?  Doggerland disappeared about 6,500 or 6,200 BCE. L11 is only about 4500 years old. I do not see Doggerland as a possible route.

The dates you present are derived using the current Variance/ASD model.  I think the data is suggesting that hidden mutations shorten the estimates while multisteps and multiple entries of a mutation lengthen it.  Further, in the ASD math, the effect of multisteps is even worse, greatly extending the time estimate.  A multistep of 4 will have 16 times more effect on the calculation than a single step would.

It is the confluence of these effects: hidden mutations on one side and multisteps and highly correlated data sets on the other which are confusing the issue and warping time.

I think Mike and I agree that over time spans of less than 1k, these effects can be compensated for.  For other, longer time frame issues, we have a problem I believe in the accuracy/precision of the current estimates.

A final thought is that I'm not fully sure that there aren't other issues.  An apparent change in data rate with modal value; specifically 388 in I1 and J2.  An apparent increase in the number of mutations for some haplotypes subjected to large physical displacements,, e.g. from one continent to another.  All of this needs to be understood, compensated for if possible and included in how we model this process.
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« Reply #201 on: April 24, 2012, 11:09:41 AM »

....  I have done a TMRCA between the Clan Gregor Moderator and  myself and the Clan Gregor chieftain.  I used two approaches: for the moderator I compared 59 STR''s and used Chandlers and the set of 110 rates from 2011. I got c. 200 AD for Chandlers rates and c. 550BC for the 110 data set.  For the chieftain, I followed Busbys recommendation and only looked at the 13 slowest FtDNA markers which we differ at two: 388 and 495.   I got a TMRCA of c. 13k BC!! I personally believe that the Chief is of Hallstatt origin who migrated to what is now Belgium and then were ousted by the Romans and they migrated to Ireland, where they became what is now called South Irish and later Dal Riadans.....
Are the Gregor Moderator and Chieftain Z253?  If they aren't, your relationship to them has to be at least two thousand years ago.

As far as using only the 13 slowest markers, per Busby, I don't recommend that at all. That's just not enough markers and particularly since you are looking for relationships in the historical timeframe I don't think the linear duration of STRs will be a big problem in your analysis.

@IronR, Mike shows the age of Z253 is around 400BC to 0AD leaving about 1500 years to L21?  Doggerland disappeared about 6,500 or 6,200 BCE. L11 is only about 4500 years old. I do not see Doggerland as a possible route.
The dates you present are derived using the current Variance/ASD model.  I think the data is suggesting that hidden mutations shorten the estimates while multisteps and multiple entries of a mutation lengthen it.  Further, in the ASD math, the effect of multisteps is even worse, greatly extending the time estimate.  A multistep of 4 will have 16 times more effect on the calculation than a single step would.
......
I think Mike and I agree that over time spans of less than 1k, these effects can be compensated for.  For other, longer time frame issues, we have a problem I believe in the accuracy/precision of the current estimates....
The dates I've calculated are based on Ken Nordtvedt's Generation 7 methodology. Ken is a former National Science Board member, appointed by President Reagan. Ken is particularly known for his mathematical abilities.  http://en.wikipedia.org/wiki/Kenneth_Nordtvedt

As an alternative method, using STR diversity "maximum likelihood" (but not statistical variance), Marko Heinila's esimates for R-L21, P312, U106 come up similar to Ken's. The interclade age for P312 and U106 is much younger than Doggerland so Z253 has to be younger than that.

I think these methods are useful for longer than 1000 years, for sure, but I don't think they are precise. Ken's methods do a nice job of giving you error ranges. Vince Vizachero has said that STR diversity is useful (linearly with time) until you get up into old haplogroup groups and he cited 25k years as an example. This is posted over in the STR Wars thread.

It is a valid argument for you to say the mutation rates that Marko and Ken use are incorrect and they should be using the evolutionary rates, rather than germ-line.  Ken is vehement in his disdain for the evolutionary rates but it is clearly an issue of disagreement. However, there is a problem with using the evolutionary rates. Using Marko and Ken's methods, they do get Hg's, like Hg I (that is pretty much European restricted) that are way too old if you use the evolutionary rates... way too old for the archaeologically documented appearance of modern man (homo sapiens sapiens) in Europe.   You are stuck in logic trap.   Your only way out is for you to argue that we must use one set of mutation rates for one haplogroup and another set for another... but we are all homo sapiens sapiens, more alike than different and the Y SNPs marking the haplogroups are just "junk DNA."  

 .... well, I guess there is the fallback that Busby used as their second line of defense - STRs are unreliable so we can't tell anything from them.  Simulations on real data show that STRs do have some consistency, though.  No one is saying they are perfectly consistent and improvements in modeling and selection shouldn't be made.
« Last Edit: April 24, 2012, 11:55:58 AM by Mikewww » Logged

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« Reply #202 on: April 24, 2012, 11:32:15 AM »

As mike has said, even the experts can't decide on the appropriate model.  I spent a lot of time on the Busby paper this winter and also pondered again the Zhivotovsky conundrum. 
There are several mathematical methodologies that produce similar results so I do want to be clear that there are alternative methods that seem to support each other in TMRCA calculations.

What is not agreed up on are the mutation rates, although the leading hobbyist-scientists seem to come down pretty much on the side of the germ-line rates...  this would include Chandler, Nordtvedt, Heinila and Klyosov. I don't know if Vizachero and Dienekes are scientists but they also are against using the evolutionary rates rather than the germ-line rates.
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Maliclavelli
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« Reply #203 on: April 24, 2012, 11:55:22 AM »

I repeat:
This posting of mine, posted here and published also by Dienekes, is waiting some response, above all from Anatole Klyosov:
An interesting haplotype of R1a1a (M17) has been found in the paper of Gunjan Sharma et al., Genetic Affinities of the Central Indian Tribal Population, PLoS one, February 2012:
DYS19=18
DYS385=14-17
DYS389=15-30
DYS390=28
DYS391=12
DYS392=14
DYS393=13
DYS437=17
DYS439=13
DYS448=22
DYS456=17
DYS458=17
At first sight it could seem we have found the R-M420 not found so far in India with its DYS492=14, which presupposes a 13, whereas all the other R1a1a haplotypes have 11 or 10 and 12 from 11, but this haplotype has been tested for M17, then it isn’t an R-M420. Also the extremely large variance of the other markers makes us think that this value 14 derives from a modal 11 (or what was the modal at the origin of this subclade). Then again all the discourses about “modal” and “variance”, as I have supported many times, are worth nothing.
But I think it would be something to say about the TMRCA of 10.97+/-1.86 kya (25 y for generation) even though calculated by the Zhivotovsky rate. It is clear that these R1a1a-s belong to different clades and the massive presence of the clade most usually found falsifies the calculation. It is clear that this haplotype is an outlier, but for this more interesting, because testifies all the mutation gone mostly for the tangent and not around the modal. If we calculate the intraclade between two of these haplotypes, for instance with this closer to the modal: 15, 11-14, 14-32, 24,10, 11, 12,14,10, 20, 15,16 we have 32 mutations. Also using the usual mutation rate of 0,0022, we have:
(454x32)/28=518
518x25=12,950
and I have used a generation of 25 years and not 32 as I use usually, and I haven’t considered other mutations around the modal.
Conclusions? The ancientness of the haplogroups is much much more than it is usually thought.

My calculation, using a germ line mutation rate, has reached results not different from the evolutionary rate of the paper, and the mistake of the paper was that of calculating the variance between haplotypes mostly of the same descent and only one (and another, but closer to the overwhelming group) outlier. The problem is to find the outliers which demonstrate all the mutations happened, and also this have had of course mutations around the modal etc. Then the evolutionary mutation rate is the unique to consider this. Also Mr Nordtvedt said many times that some hg.I of his had an  ancientness of 6000 years, but the node with the closest branch was at least 20000 years old. It happened simply that the intermediate haplotypes died, but, fortunately, it happens that sometimes someone survives.
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« Reply #204 on: April 24, 2012, 12:03:30 PM »

I repeat:
This posting of mine, posted here and published also by Dienekes, is waiting some response, above all from Anatole Klyosov:
An interesting haplotype of R1a1a (M17) has been found in the paper of Gunjan Sharma et al., Genetic Affinities of the Central Indian Tribal Population, PLoS one, February 2012:....

Using a single example to argue against large scale studies and mathematical analysis is a poor argument technique known as the "exception fallacy." http://changingminds.org/disciplines/argument/fallacies/exception.htm

Why are we posting an R1a1a question in the Z226 thread?  

RMS2, can you move the side discussions on STR diversity, TMRCA methodologies and mutation rates over to a separate thread? Please just do it on the fly as they come up. You can use the STR Wars thread if you want although I really didn't intend for it to get into mutation rates.  We just need to have a place to steer these side conversations.  I don't plan on letting some of these items go unchallenged and I'm sure others want to challenge me... that's fine but let's put those things in their own thread.
« Last Edit: April 24, 2012, 12:12:48 PM by Mikewww » Logged

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Maliclavelli
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« Reply #205 on: April 24, 2012, 12:09:20 PM »

Which fallacy is yours? That of the authority or, better, that of the moderator?
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Maliclavelli


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« Reply #206 on: April 24, 2012, 12:10:49 PM »

Which fallacy is yours? That of the authority or, better, that of the moderator?

You are the giant slayer who can read others thoughts and speak on behalf of those you don't know.   I don't see why you need to ask questions since you know the answers.

Please start up a separate thread to explain your thinking and challenges. Some of this is completely off topic.
« Last Edit: April 24, 2012, 12:12:03 PM by Mikewww » Logged

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« Reply #207 on: April 24, 2012, 12:21:33 PM »

Here another fallacy, the “off topic one”. It remains to you the “fallacy of fallacy”, then, like Hegel taught, you will have reached the irony, Ein Nichtiges an Sich Vernichtendes.
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Maliclavelli


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ironroad41
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« Reply #208 on: April 24, 2012, 12:38:09 PM »

As mike has said, even the experts can't decide on the appropriate model.  I spent a lot of time on the Busby paper this winter and also pondered again the Zhivotovsky conundrum. 
There are several mathematical methodologies that produce similar results so I do want to be clear that there are alternative methods that seem to support each other in TMRCA calculations.

What is not agreed up on are the mutation rates, although the leading hobbyist-scientists seem to come down pretty much on the side of the germ-line rates...  this would include Chandler, Nordtvedt, Heinila and Klyosov. I don't know if Vizachero and Dienekes are scientists but they also are against using the evolutionary rates rather than the germ-line rates.
I am responding to your previous post and this one.  We are all homosapiens, but what does that mean?  We have many differences due to environment and evolution.  The same is true in this area of study.  If you have accessed the table I referred to you can look at the distribution of 388 for hgs I1, J2, and R1b.  I am emphasizing this dys loci because its behavior can significantly affect the TMRCA estimate.  For this loci Chandler gives a value of .00022 per gen and burgurella .00046.  From the table I note that R1b had approximately 221 mutations out of 22129 entries.  We have no idea how many are unique and how many are inherited.  J2 had 265 out of 915 and I had 2508 out of 5700!  Additionally the data spread is across 5 to 6 values for I and J2 and across essentially 3 values for R1b. In no way can one rate support these data.   Additionally, the variance calculation will show a large contribution to TMRCA due to the very low mutation rate and concomitant long time period expected between mutations at this locus.  No wonder I and J appear older in Kens work.

I really believe you have to get into this level of detail to understand the Y STR mutation process and its current problems.  Most Dys loci who mutate within the modal +/- l generate no appreciable variance and certainly no increase occurs with time as the drunkards walk model suggests.  Most of the variance is generated by multisteps, especially steps greater than 2 and the faster mutators such as CDYa,b.

My conclusion is that the Variance/ASD model does not represent the data properties.
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« Reply #209 on: April 24, 2012, 01:14:30 PM »

I am responding to your previous post and this one.  We are all homosapiens, but what does that mean?  ...
I'll respond over in the STR Wars thread when I get a chance.  We are actually Homo sapiens sapiens...  at least I hope.
Quote
"Modern humans" are defined as the Homo sapiens species, of which the only extant subspecies is known as Homo sapiens sapiens
http://en.wikipedia.org/wiki/Human
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« Reply #210 on: April 25, 2012, 03:42:23 PM »

... . That said, I will continue to argue that my haplotype is different than most R-L21's and began quite early in the R-L21 cycle. JMHO

I copied this from another thread, because it is pertinent to Z253 overall. I think your haplotype demonstrates that you are in an early branch off of from the Irish III and Irish IV lineages within Z253.... and that Z253 is quite old. It can't be older than L21 but it is trending back that way.

...
For what its worth, McGregor, I looked at Mikew L21Ext sheet and selecting only Z253 tested Hts (n=32) here is what I see is that your closest 111 marker Z253 kit is a GD of 29 up to 50 (TMRCA range of 1784 to 3075 years). Most of the markers that you are different are in the 68-111 panel.

No one close to you. Outlier your are until others are found and are Z253 positive. Keep hunting. MJost...
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« Reply #211 on: April 30, 2012, 07:05:34 AM »

R-Z253 (L226-) acquired yet a third French member as of this morning: Grenier (kit 79112, Ysearch 4XHJC). He has no close matches at 67 markers in FTDNA's database. His closest matches at 37 markers are 4 off.
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« Reply #212 on: April 30, 2012, 09:28:33 AM »

Steve,

f79112 Grenier France EW Fra North & Central
 
is closest GD9/67 with

f41327 Berryman   R-L21/Z253* England IS Eng South West

his next closest starts as GD18.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #213 on: April 30, 2012, 10:41:59 AM »

Steve,

f79112 Grenier France EW Fra North & Central
 
is closest GD9/67 with

f41327 Berryman   R-L21/Z253* England IS Eng South West

his next closest starts as GD18.

MJost


Theoretically, that puts him and Berriman sharing a common ancestor roughly around the time of the Norman Conquest.

That makes sense historically, at least, if Berriman is descended from a Norman or a Breton.
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« Reply #214 on: April 30, 2012, 01:40:34 PM »

With the dominating surname Grenier in France according to http://worldnames.publicprofiler.org you would have to believe Berryman is French YDNA as Berryman has such a very low numbers in Wales and England.

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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #215 on: April 30, 2012, 01:47:33 PM »

Here is a good site for checking French surnames. Notice that Grenier is most common in Seine Maritime in Haute Normandie, so it is evidently a Norman surname.
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« Reply #216 on: April 30, 2012, 03:04:45 PM »

Now that shows that mainland Normandy in France is a big cluster of Grenier's. Notice the large number in the Southwest Gironde and along a central west to east area.
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #217 on: April 30, 2012, 03:14:26 PM »

Now that shows that mainland Normandy in France is a big cluster of Grenier's. Notice the large number in the Southwest Gironde and along a central west to east area.

I noticed, but Haute Normandie has by far the most Greniers, and, relative to our Grenier, probably the most L21 (although Gironde is probably not lacking in L21 either).

Normandy makes sense historically, as well, given that Berriman and Grenier are haplotype neighbors (I don't want to say "matches" - they aren't all that close).

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« Reply #218 on: April 30, 2012, 03:43:54 PM »

Looking at there marker values, they each have three different markers that do not match but they have many (8) common or same direction off-modal allele values.

I would say yes they are in a border geneological time frame from the same lineage looking at that with fact that they are now the same subclade.



 
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #219 on: April 30, 2012, 04:13:35 PM »

16 of 43 L253*/** that have an identified location are from various areas in Ireland. There is a large important need for Coastal Norman's to be tested.
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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« Reply #220 on: June 14, 2012, 04:43:13 PM »

Wow it only gets better, or at least deeper.

Quote from: Greg M
The anonymous researcher and I have been working, with some sample classification assistance from Rich Rocca and Ray Banks, to analyze the latest data from the 1000 Genomes Project as it pertains to R-L21. The analysis has allowed identification of two groups under Z253.

    One of the groups joins NA06984 (CEU, Utahn of European ancestry) and HG01500 (IBS, Iberian from Spain). There are six high-quality candidate variants that these samples seem to share. One of these is already in FTDNA's ymap as L1066. The other variants have been assigned names Z2182 through Z2186.
    The second group joins HG01503 and HG01675 (both IBS, Iberian from Spain). There are 21 high-quality candidate variants that these samples seem to share. One, DF73, has been explored by the anonymous researcher, but he did not find any derived individuals based on testing a very small number of separate (i.e. non-1000 Genomes Project) Z253+ samples, so this remains an unconfirmed candidate variant at present. The other candidate variants have been given names Z2187 through Z2206. Because of the large number of variants shared by these samples, it is quite possible they may span a spectrum of frequency with many being "semi-private".

An updated phylogeny depicting the proposed placement of these candidate variants is at https://www.box.com/s/1384cf752f6acbc5be03 . The newest samples that have been added with the first batch of "Phase II" data from the 1000 Genomes Project are highlighted in red.
http://tech.groups.yahoo.com/group/RL21Project/message/8768

Thanks once again to the anonymous researcher and Richard R along with Greg M and Ray Banks. You are better than the "dream team".
« Last Edit: June 14, 2012, 05:02:31 PM by Mikewww » Logged

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« Reply #221 on: July 25, 2012, 10:02:12 PM »

I finally moved all the guys in that Spanish cluster with 385=12-14 and 459=10-10 (among other identifying markers) to the R-Z253 category. Don't know why I waited this long. I think I just kind of forgot about it.

Anyway, one guy who is kind of on the fringe of it, Robles, kit 67597, has ordered Z253.

And I ordered it yesterday myself, which renews my interest in it (unless and until I get a negative result, that is).
« Last Edit: July 25, 2012, 10:06:22 PM by rms2 » Logged

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« Reply #222 on: July 26, 2012, 09:40:36 AM »

Good Luck Rich.

Though I am happy to have your company at DF13*

I'm not sure whats next for me.
« Last Edit: July 26, 2012, 09:41:20 AM by OConnor » Logged

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R-DF13**(L21>DF13)
M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, M173+, M269+, M343+, P312+, L21+, DF13+, M207+, P25+, L11+, L138+, L141+, L15+, L150+, L16+, L23+, L51+, L52+, M168+, M173+, M207+, M213+, M269+, M294+, M299+, M306+, M343+, P69+, P9.1+, P97+, PK1+, SRY10831.1+, L21+, L226-, M37-, M222-, L96-, L193-, L144-, P66-, SRY2627-, M222-, DF49-, L371-, DF41-, L513-, L555-, L1335-, L1406-, Z251-, L526-, L130-, L144-, L159.2-, L192.1-, L193-, L195-, L96-, DF21-, Z255-, DF23-, DF1-, Z253-, M37-, M65-, M73-, M18-, M126-, M153-, M160-, P66-

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« Reply #223 on: July 26, 2012, 10:00:28 AM »

Good Luck Rich.

Though I am happy to have your company at DF13*

I'm not sure whats next for me.

Thanks, Mike. I'm not sure what my chances of being Z253+ are. Probably not good.

Thus far, you and I have kept pace since 2006 with always the same results. I remember you were one of the first to congratulate me when I got my first 37-marker results and was told I was "R1b1".

« Last Edit: July 26, 2012, 10:02:39 AM by rms2 » Logged

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« Reply #224 on: July 26, 2012, 10:55:14 AM »

Good Luck Rich.

Though I am happy to have your company at DF13*

I'm not sure whats next for me.

Thanks, Mike. I'm not sure what my chances of being Z253+ are. Probably not good.

Thus far, you and I have kept pace since 2006 with always the same results. I remember you were one of the first to congratulate me when I got my first 37-marker results and was told I was "R1b1".

Z253 is full of surprises so you never know...
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
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